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UniProtKB - P38506 (XNI_ECOLI)

Entry version 152 (10 Feb 2021)
Sequence version 3 (24 Nov 2009)
Previous versions | rss
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Protein

Flap endonuclease Xni

Gene

ygdG

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Has flap endonuclease activity (PubMed:23821668), but does not seem to have exonuclease activity (PubMed:17567612 and PubMed:19000038). During DNA replication, flap endonucleases cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment.3 Publications

Caution

Was initially reported (PubMed:9592142) as a 3'-5' exonuclease due to contamination of samples. This protein possesses no such activity (PubMed:17567612 and PubMed:19000038).1 Publication

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Protein has several cofactor binding sites:

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi104Magnesium1
Metal bindingi171Potassium; via carbonyl oxygen1
Metal bindingi172Potassium; via carbonyl oxygen1
Metal bindingi180Potassium; via carbonyl oxygen1
Metal bindingi182Potassium; via carbonyl oxygen1
Metal bindingi185Potassium; via carbonyl oxygen1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionDNA-binding, Endonuclease, Hydrolase, Nuclease
LigandMagnesium, Metal-binding, Potassium

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:EG12372-MONOMER

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Flap endonuclease Xni (EC:3.1.-.-)
Short name:
FEN
Alternative name(s):
Exonuclease IX
Short name:
ExoIX
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:ygdG
Synonyms:exo, xni
Ordered Locus Names:b2798, JW5446
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Can be deleted, however double-disruptions of polA and xni are not viable, suggesting they have a redundant essential function.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi67K → A: Strongly reduces flap endonuclease activity. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001012921 – 251Flap endonuclease XniAdd BLAST251

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P38506

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P38506

PRoteomics IDEntifications database

More...PRIDEi		P38506

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Interacts with the DNA-binding proteins SSB and H-NS.

1 Publication

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		4259222, 102 interactors
851586, 1 interactor

Database of interacting proteins

More...DIPi		DIP-11145N

Protein interaction database and analysis system

More...IntActi		P38506, 3 interactors

STRING: functional protein association networks

More...STRINGi		511145.b2798

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P38506

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini160 – 2495'-3' exonucleaseSequence analysisAdd BLAST90

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni184 – 189Interaction with DNA6

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and domains' section denotes the positions of regions of coiled coil within the protein.<p><a href='/help/coiled' target='_top'>More...</a></p>Coiled coili198 – 225Sequence analysisAdd BLAST28

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the Xni family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG0258, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_004675_1_2_6

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P38506

Database for complete collections of gene phylogenies

More...PhylomeDBi		P38506

Family and domain databases

Conserved Domains Database

More...CDDi		cd09898, H3TH_53EXO, 1 hit

HAMAP database of protein families

More...HAMAPi		MF_01192, Xni, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR020046, 5-3_exonucl_a-hlix_arch_N
IPR002421, 5-3_exonuclease
IPR036279, 5-3_exonuclease_C_sf
IPR020045, DNA_polI_H3TH
IPR038969, FEN
IPR008918, HhH2
IPR029060, PIN-like_dom_sf
IPR022895, Xni

The PANTHER Classification System

More...PANTHERi		PTHR42646, PTHR42646, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF01367, 5_3_exonuc, 1 hit
PF02739, 5_3_exonuc_N, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00475, 53EXOc, 1 hit
SM00279, HhH2, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF47807, SSF47807, 1 hit
SSF88723, SSF88723, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P38506-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAVHLLIVDA LNLIRRIHAV QGSPCVETCQ HALDQLIMHS QPTHAVAVFD 
        60         70         80         90        100
DENRSSGWRH QRLPDYKAGR PPMPEELHDE MPALRAAFEQ RGVPCWSTSG 
       110        120        130        140        150
NEADDLAATL AVKVTQAGHQ ATIVSTDKGY CQLLSPTLRI RDYFQKRWLD 
       160        170        180        190        200
APFIDKEFGV QPQQLPDYWG LAGISSSKVP GVAGIGPKSA TQLLVEFQSL 
       210        220        230        240        250
EGIYENLDAV AEKWRKKLET HKEMAFLCRD IARLQTDLHI DGNLQQLRLV 

R
Length:251
Mass (Da):28,166
Last modified:November 24, 2009 - v3
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i937A2CDCC58B03A5
GO

<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence AAB40448 differs from that shown. Reason: Erroneous initiation. Extended N-terminus.Curated
The sequence BAE76870 differs from that shown. Reason: Erroneous initiation. Extended N-terminus.Curated

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
L07763 Genomic DNA No translation available.
U29581 Genomic DNA Translation: AAB40448.1 Different initiation.
U00096 Genomic DNA Translation: AAC75840.2
AP009048 Genomic DNA Translation: BAE76870.1 Different initiation.
M27177 Genomic DNA No translation available.

Protein sequence database of the Protein Information Resource

More...PIRi		B65062

NCBI Reference Sequences

More...RefSeqi		NP_417278.4, NC_000913.3
WP_000268232.1, NZ_SSUV01000026.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC75840; AAC75840; b2798
BAE76870; BAE76870; BAE76870

Database of genes from NCBI RefSeq genomes

More...GeneIDi		57730398
947256

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW5446
eco:b2798

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.3935

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L07763 Genomic DNA No translation available.
U29581 Genomic DNA Translation: AAB40448.1 Different initiation.
U00096 Genomic DNA Translation: AAC75840.2
AP009048 Genomic DNA Translation: BAE76870.1 Different initiation.
M27177 Genomic DNA No translation available.
PIRiB65062
RefSeqiNP_417278.4, NC_000913.3
WP_000268232.1, NZ_SSUV01000026.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3ZD8X-ray2.00A/B1-251[»]
3ZD9X-ray2.00A1-251[»]
3ZDAX-ray1.50A1-251[»]
3ZDBX-ray1.47A1-251[»]
3ZDCX-ray1.53A1-251[»]
3ZDDX-ray1.50A1-251[»]
3ZDEX-ray2.45A1-251[»]
SMRiP38506
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi4259222, 102 interactors
851586, 1 interactor
DIPiDIP-11145N
IntActiP38506, 3 interactors
STRINGi511145.b2798

Proteomic databases

jPOSTiP38506
PaxDbiP38506
PRIDEiP38506

Genome annotation databases

EnsemblBacteriaiAAC75840; AAC75840; b2798
BAE76870; BAE76870; BAE76870
GeneIDi57730398
947256
KEGGiecj:JW5446
eco:b2798
PATRICifig|1411691.4.peg.3935

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...EchoBASEi		EB2275

Phylogenomic databases

eggNOGiCOG0258, Bacteria
HOGENOMiCLU_004675_1_2_6
InParanoidiP38506
PhylomeDBiP38506

Enzyme and pathway databases

BioCyciEcoCyc:EG12372-MONOMER

Miscellaneous databases

Protein Ontology

More...PROi		PR:P38506

Family and domain databases

CDDicd09898, H3TH_53EXO, 1 hit
HAMAPiMF_01192, Xni, 1 hit
InterProiView protein in InterPro
IPR020046, 5-3_exonucl_a-hlix_arch_N
IPR002421, 5-3_exonuclease
IPR036279, 5-3_exonuclease_C_sf
IPR020045, DNA_polI_H3TH
IPR038969, FEN
IPR008918, HhH2
IPR029060, PIN-like_dom_sf
IPR022895, Xni
PANTHERiPTHR42646, PTHR42646, 1 hit
PfamiView protein in Pfam
PF01367, 5_3_exonuc, 1 hit
PF02739, 5_3_exonuc_N, 1 hit
SMARTiView protein in SMART
SM00475, 53EXOc, 1 hit
SM00279, HhH2, 1 hit
SUPFAMiSSF47807, SSF47807, 1 hit
SSF88723, SSF88723, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiXNI_ECOLI
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P38506
Secondary accession number(s): Q2MA36, Q46922
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: November 24, 2009
Last modified: February 10, 2021
This is version 152 of the entry and version 3 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
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